Microbes have demonstrated remarkable potential for Sr2+ bioremediation under both laboratory and in situ conditions. However, the mechanism for efficient biological removal of toxic elements remains elusive. This study systematically investigated the efficacy and underlying mechanisms of Sr2+ immobilization through microbially induced carbonate precipitation (MICP) using Sporosarcina pasteurii in a simulated contaminated system. Experimental results revealed that the strain achieved simultaneous and efficient immobilization of both Sr2+ and Ca2+ within 72 h, with removal efficiencies exceeding 99.95 %. Solution chemistry analysis identified high concentrations of carbonate and bicarbonate ions, generated through bacterial ureolysis, as the key drivers of the efficient precipitation process. XRD, EDS, and XPS analyses confirmed the incorporation of Sr2+ into crystal lattices of calcite and strontianite crystal lattices through isomorphic substitution. Intriguingly, the Sr/Ca molar ratio (0.4–0.6) in early-stage precipitates was substantially different from that in the initial solution. Complementary analyses using FTIR and 3D-EEM fluorescence spectroscopy further demonstrated that bacterial-secreted organic matter selectively regulated the preferential precipitation of Ca2+. As a result, the strain's exceptional mineralization capacity effectively compensated for this preferential effect, ensuring efficient Sr2+ immobilization. This study demonstrates the application advantages of microbes in MICP technology, providing critical insights for the remediation of radioactive contamination as well as a promising strategy for carbon sequestration of microbe-derived organic matter.